Indirect cost of chronic diseases have received increasing attention since recent diagnostic and therapeutic improvements have markedly raised costs of care. Relevant cost savings can be expected through the reduction of indirect costs. However, the assessment methods of indirect cost components still differ widely, leading to heterogeneous data that do not allow for a direct comparison. This prospective study of gainfully employed patients suffering from rheumatoid arthritis aims to compare indirect costs assessed by different current methodological approaches (human capital and friction cost method valued by either population or individual data), and compare the methods employed in order to provide a proposal for the standardization of indirect cost assessment. The finding of the present investigation underline the importance to define standardized assessment methods for a comparison of the results of cost evaluations comprising indirect costs. A recommendation for the assessment of productivity losses and their valuation is given. In a given specific economic investigation, the optimal assessment method might differ from these general statements. These recommendations are proposed to give an orientation in a field of heterogeneous strategies in order to improve comparability of indirect cost assessment.